TB-Profiler result

Run: ERR4816031
Summary

Run ID: ERR4816031

Sample name:

Date: 20-10-2023 07:59:41

Number of reads: 1845365

Percentage reads mapped: 96.61

Strain: lineage4.3.3

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7850 c.549C>G synonymous_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619734 c.-157C>A upstream_gene_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779379 c.-899C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.36
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.4
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.43
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.43
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.55
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.62
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.64
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.81
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.74
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.74
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.65
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.57
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.57
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.48
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.43
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.48
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.48
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.45
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.35
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.44
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.35
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.48
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.46
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.48
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.46
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.46
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169044 c.1569G>C synonymous_variant 0.67
PPE35 2169047 p.Ile522Val missense_variant 0.64
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169056 c.1557A>G synonymous_variant 0.64
PPE35 2169063 p.Met517Thr missense_variant 1.0
PPE35 2169071 c.1542A>G synonymous_variant 0.58
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407865 c.337delG frameshift_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0